Methods and kits for labeling cellular molecules

ABSTRACT

Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a Track 1 continuation of co-pending U.S. patentapplication Ser. No. 17/695,671, filed Mar. 15, 2022, which is a Track 1continuation of co-pending U.S. application Ser. No. 17/521,263, filedNov. 8, 2021, which is a Track 1 continuation of U.S. patent applicationSer. No. 17/249,257, filed Feb. 25, 2021, now U.S. Pat. No. 11,168,355,issued Nov. 9, 2021, which is a Track 1 continuation of co-pending U.S.patent application Ser. No. 17/122,321, filed Dec. 15, 2020, which is acontinuation of U.S. patent application Ser. No. 14/941,433, filed Nov.13, 2015, now U.S. Pat. No. 10,900,065, issued Jan. 26, 2021, whichclaims the benefit of U.S. Provisional Application No. 62/080,055, filedNov. 14, 2014, now expired, each of which is hereby incorporated byreference in its entirety.

STATEMENT OF GOVERNMENT LICENSE RIGHTS

This invention was made with government support under Grant No. R01CA207029, awarded by the National Institutes of Health, and Grant No.CCF-1317653, awarded by the National Science Foundation. The governmenthas certain rights in the invention.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing XML associated with this application is provided inXML format and is hereby incorporated by reference into thespecification. The name of the XML file containing the sequence listingis 3915_P1043US_CON6_UW_Seq_List_20220725_ST26.txt. The XML file is 8KB; was created on Jul. 20, 2022; and is being submitted electronicallyvia Patent Center with the filing of the specification.

TECHNICAL FIELD

The present disclosure relates generally to methods of uniquely labelingor barcoding molecules within a cell, a plurality of cells, and/or atissue. The present disclosure also relates to kits for uniquelylabeling molecules within a cell, a plurality of cells, and/or a tissue.In particular, the methods and kits may relate to the labeling of RNAs,cDNAs, DNAs, proteins, peptides, and/or antigens.

BACKGROUND

Next Generation Sequencing (NGS) can be used to identify and/or quantifyindividual transcripts from a sample of cells. However, such techniquesmay be too complicated to perform on individual cells in large samples.In such methods, RNA transcripts are generally purified from lysed cells(i.e., cells that have been broken apart), followed by conversion of theRNA transcripts into complementary DNA (cDNA) using reversetranscription. The cDNA sequences can then be sequenced using NGS. Insuch a procedure, all of the cDNA sequences are mixed together beforesequencing, such that RNA expression is measured for a whole sample andindividual sequences cannot be linked back to an individual cell.

Methods for uniquely labeling or barcoding transcripts from individualcells can involve the manual separation of individual cells intoseparate reaction vessels and can require specialized equipment. Analternative approach to sequencing individual transcripts in cells is touse microscopy to identify individual fluorescent bases. However, thistechnique can be difficult to implement and limited to sequencing a lownumber of cells.

BRIEF DESCRIPTION OF THE DRAWINGS

The embodiments disclosed herein will become more fully apparent fromthe following description and appended claims, taken in conjunction withthe accompanying drawings.

FIG. 1 depicts ligation of nucleic acid tags to form a label or barcode.

FIG. 2 is a schematic representation of the formation of cDNA by in situreverse transcription. Panel A depicts a cell that is fixed andpermeabilized. Panel B depicts addition of a poly(T) primer, which cantemplate the reverse transcription of polyadenylated transcripts. PanelC depicts addition of a random hexamer, which can template the reversetranscription of substantially any transcript. Panel D depicts theaddition of a primer that is designed to target a specific transcriptsuch that only a subset of transcripts may be amplified. Panel E depictsthe cell of Panel A after reverse transcription, illustrating a cDNAhybridized to an RNA.

FIG. 3A depicts non-templated ligation of a single-stranded adapter toan RNA fragment.

FIG. 3B depicts ligation of a single-stranded adapter using a partialduplex with random hexamer primers.

FIG. 4 depicts primer binding.

FIG. 5 depicts primer binding followed by reverse transcription.

FIG. 6 depicts DNA-tagged antibodies for use in labeling cellularproteins.

FIG. 7 depicts aptamers for use in labeling cellular proteins.

FIG. 8 is a schematic representation of the dividing, tagging, andpooling of cells, according to an embodiment of the present disclosure.As depicted, cells can be divided between a plurality of reactionvessels. One cell is highlighted to show its path through theillustrated process.

FIG. 9A depicts an exemplary workflow, according to an embodiment of thepresent disclosure.

FIG. 9B depicts an exemplary workflow, according to another embodimentof the present disclosure.

FIG. 10 depicts a reverse transcription primer (BC_0055), according toan embodiment of the present disclosure.

FIG. 11 depicts an annealed, first-round barcode oligo, according to anembodiment of the present disclosure.

FIG. 12 depicts an annealed, second-round barcode oligo, according to anembodiment of the present disclosure.

FIG. 13 depicts an annealed, third-round barcode oligo, according to anembodiment of the present disclosure.

FIG. 14 depicts ligation stop oligos, according to an embodiment of thepresent disclosure.

FIG. 15 depicts a single-stranded DNA adapter oligo (BC_0047) ligated tothe 3′ end of a cDNA, according to an embodiment of the presentdisclosure.

FIG. 16 depicts a PCR product formed using primers BC_0051 and BC_0062and the 3′ adapter oligo (BC_0047) after it has been ligated to barcodedcDNA.

FIG. 17 depicts BC_0027, which includes the flow cell binding sequenceand the binding site for the TRUSEQ™ read 1 primer and BC_0063, whichincludes the flow cell binding sequence and the TruSeq multiplex read 2and index binding sequence. FIG. 17 also illustrates a region for asample index, which is GATCTG in this embodiment.

FIG. 18 is a scatter plot, wherein for each unique barcode combinationthe number of reads aligning to the human genome (x-axis) and the mousegenome (y-axis) are plotted.

DETAILED DESCRIPTION

The present disclosure relates generally to methods of uniquely labelingor barcoding molecules within a cell, a plurality of cells, and/or atissue. The present disclosure also relates to kits for uniquelylabeling or barcoding molecules within a cell, a plurality of cells,and/or a tissue. The molecules to be labeled may include, but are notlimited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

It will be readily understood that the embodiments, as generallydescribed herein, are exemplary. The following more detailed descriptionof various embodiments is not intended to limit the scope of the presentdisclosure, but is merely representative of various embodiments.Moreover, the order of the steps or actions of the methods disclosedherein may be changed by those skilled in the art without departing fromthe scope of the present disclosure. In other words, unless a specificorder of steps or actions is required for proper operation of theembodiment, the order or use of specific steps or actions may bemodified.

The term “binding” is used broadly throughout this disclosure to referto any form of attaching or coupling two or more components, entities,or objects. For example, two or more components may be bound to eachother via chemical bonds, covalent bonds, ionic bonds, hydrogen bonds,electrostatic forces, Watson-Crick hybridization, etc.

A first aspect of the disclosure relates to methods of labeling nucleicacids. In some embodiments, the methods may comprise labeling nucleicacids in a first cell. The methods may comprise: (a) generatingcomplementary DNAs (cDNAs) within a plurality of cells comprising thefirst cell by reverse transcribing RNAs using a reverse transcriptionprimer comprising a 5′ overhang sequence; (b) dividing the plurality ofcells into a number (n) of aliquots; (c) providing a plurality ofnucleic acid tags to each of the n aliquots, wherein each labelingsequence of the plurality of nucleic acid tags provided into a givenaliquot is the same, and wherein a different labeling sequence isprovided into each of the n aliquots; (d) binding at least one of thecDNAs in each of the n aliquots to the nucleic acid tags; (e) combiningthe n aliquots; and (f) repeating steps (b), (c), (d), and (e) with thecombined aliquot. In various embodiments, the plurality of cells may beselected from eukaryotic cells and prokaryotic cells. In various otherembodiments, the plurality of cells may be selected from, but notlimited to, at least one of mammalian cells, yeast cells, and/orbacterial cells.

In certain embodiments, each nucleic acid tag may comprise a firststrand including a 3′ hybridization sequence extending from a 3′ end ofa labeling sequence and a 5′ hybridization sequence extending from a 5′end of the labeling sequence. Each nucleic acid tag may also comprise asecond strand including an overhang sequence. The overhang sequence mayinclude (i) a first portion complementary to at least one of the 5′hybridization sequence and the 5′ overhang sequence and (ii) a secondportion complementary to the 3′ hybridization sequence. In someembodiments, the nucleic acid tag (e.g., the final nucleic acid tag) maycomprise a capture agent such as, but not limited to, a 5′ biotin. AcDNA labeled with a 5′ biotin-comprising nucleic acid tag may allow orpermit the attachment or coupling of the cDNA to a streptavidin-coatedmagnetic bead. In some other embodiments, a plurality of beads may becoated with a capture strand (i.e., a nucleic acid sequence) that isconfigured to hybridize to a final sequence overhang of a barcode. Inyet some other embodiments, cDNA may be purified or isolated by use of acommercially available kit (e.g., an RNEASY™ kit).

In various embodiments, step (f) (i.e., steps (b), (c), (d), and (e))may be repeated a number of times sufficient to generate a unique seriesof labeling sequences for the cDNAs in the first cell. Stated anotherway, step (f) may be repeated a number of times such that the cDNAs inthe first cell may have a first unique series of labeling sequences, thecDNAs in a second cell may have a second unique series of labelingsequences, the cDNAs in a third cell may have a third unique series oflabeling sequences, and so on. The methods of the present disclosure mayprovide for the labeling of cDNA sequences from single cells with uniquebarcodes, wherein the unique barcodes may identify or aid in identifyingthe cell from which the cDNA originated. In other words, a portion, amajority, or substantially all of the cDNA from a single cell may havethe same barcode, and that barcode may not be repeated in cDNAoriginating from one or more other cells in a sample (e.g., from asecond cell, a third cell, a fourth cell, etc.).

In some embodiments, barcoded cDNA can be mixed together and sequenced(e.g., using NGS), such that data can be gathered regarding RNAexpression at the level of a single cell. For example, certainembodiments of the methods of the present disclosure may be useful inassessing, analyzing, or studying the transcriptome (i.e., the differentRNA species transcribed from the genome of a given cell) of one or moreindividual cells.

As discussed above, an aliquot or group of cells can be separated intodifferent reaction vessels or containers and a first set of nucleic acidtags can be added to the plurality of cDNA transcripts. The aliquots ofcells can then be regrouped, mixed, and separated again and a second setof nucleic acid tags can be added to the first set of nucleic acid tags.In various embodiments, the same nucleic acid tag may be added to morethan one aliquot of cells in a single or given round of labeling.However, after repeated rounds of separating, tagging, and repooling,the cDNAs of each cell may be bound to a unique combination or sequenceof nucleic acid tags that form a barcode. In some embodiments, cells ina single sample may be separated into a number of different reactionvessels. For example, the number of reaction vessels may include four1.5 ml microcentrifuge tubes, a plurality of wells of a 96-well plate,or another suitable number and type of reaction vessels.

In certain embodiments, step (f) (i.e., steps (b), (c), (d), and (e))may be repeated a number of times wherein the number of times isselected from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, etc. In certain other embodiments, step (f) may berepeated a sufficient number of times such that the cDNAs of each cellwould be likely to be bound to a unique barcode. The number of times maybe selected to provide a greater than 50% likelihood, greater than 90%likelihood, greater than 95% likelihood, greater than 99% likelihood, orsome other probability that the cDNAs in each cell are bound to a uniquebarcode. In yet other embodiments, step (f) may be repeated some othersuitable number of times.

In some embodiments, the methods of labeling nucleic acids in the firstcell may comprise fixing the plurality of cells prior to step (a). Forexample, components of a cell may be fixed or cross-linked such that thecomponents are immobilized or held in place. The plurality of cells maybe fixed using formaldehyde in phosphate buffered saline (PBS). Theplurality of cells may be fixed, for example, in about 4% formaldehydein PBS. In various embodiments, the plurality of cells may be fixedusing methanol (e.g., 100% methanol) at about −20° C. or at about 25° C.In various other embodiments, the plurality of cells may be fixed usingmethanol (e.g., 100% methanol), at between about −20° C. and about 25°C. In yet various other embodiments, the plurality of cells may be fixedusing ethanol (e.g., about 70-100% ethanol) at about −20° C. or at roomtemperature. In yet various other embodiments, the plurality of cellsmay be fixed using ethanol (e.g., about 70-100% ethanol) at betweenabout −20° C. and room temperature. In still various other embodiments,the plurality of cells may be fixed using acetic acid, for example, atabout −20° C. In still various other embodiments, the plurality of cellsmay be fixed using acetone, for example, at about −20° C. Other suitablemethods of fixing the plurality of cells are also within the scope ofthis disclosure.

In certain embodiments, the methods of labeling nucleic acids in thefirst cell may comprise permeabilizing the plurality of cells prior tostep (a). For example, holes or openings may be formed in outermembranes of the plurality of cells. TRITON™ X-100 may be added to theplurality of cells, followed by the addition of HCl to form the one ormore holes. About 0.2% TRITON™ X-100 may be added to the plurality ofcells, for example, followed by the addition of about 0.1 N HCl. Incertain other embodiments, the plurality of cells may be permeabilizedusing ethanol (e.g., about 70% ethanol), methanol (e.g., about 100%methanol), Tween 20 (e.g., about 0.2% Tween 20), and/or NP-40 (e.g.,about 0.1% NP-40). In various embodiments, the methods of labelingnucleic acids in the first cell may comprise fixing and permeabilizingthe plurality of cells prior to step (a).

In some embodiments, the cells may be adherent cells (e.g., adherentmammalian cells). Fixing, permeabilizing, and/or reverse transcriptionmay be conducted or performed on adherent cells (e.g., on cells that areadhered to a plate). For example, adherent cells may be fixed,permeabilized, and/or undergo reverse transcription followed bytrypsinization to detach the cells from a surface. Alternatively, theadherent cells may be detached prior to the separation and/or taggingsteps. In some other embodiments, the adherent cells may be trypsinizedprior to the fixing and/or permeabilizing steps.

In some embodiments, the methods of labeling nucleic acids in the firstcell may comprise ligating at least two of the nucleic acid tags thatare bound to the cDNAs. Ligation may be conducted before or after thelysing and/or the cDNA purification steps. Ligation can comprisecovalently linking the 5′ phosphate sequences on the nucleic acid tagsto the 3′ end of an adjacent strand or nucleic acid tag such thatindividual tags are formed into a continuous, or substantiallycontinuous, barcode sequence that is bound to the 3′ end of the cDNAsequence. In various embodiments, a double-stranded DNA or RNA ligasemay be used with an additional linker strand that is configured to holda nucleic acid tag together with an adjacent nucleic acid in a “nicked”double-stranded conformation. The double-stranded DNA or RNA ligase canthen be used to seal the “nick.” In various other embodiments, asingle-stranded DNA or RNA ligase may be used without an additionallinker. In certain embodiments, the ligation may be performed within theplurality of cells

FIG. 1 illustrates ligation of a plurality of nucleic acid tags to forma substantially continuous label or barcode. For example, after aplurality of nucleic acid tag additions, each cDNA transcript may bebound or linked to series of nucleic acid tags. Use of a ligase mayligate or covalently link a portion of the nucleic acid tags to form asubstantially continuous label or barcode that is bound or attached to acDNA transcript.

In certain other embodiments, the methods may comprise lysing theplurality of cells (i.e., breaking down the cell structure) to releasethe cDNAs from within the plurality of cells, for example, after step(f). In some embodiments, the plurality of cells may be lysed in a lysissolution (e.g., 10 mM Tris-HCl (pH 7.9), 50 mM EDTA (pH 7.9), 0.2 MNaCl, 2.2% SDS, 0.5 mg/ml ANTI-RNase (a protein ribonuclease inhibitor;AMBION®) and 1000 mg/ml proteinase K (AMBION®)), for example, at about55° C. for about 3 hours with shaking (e.g., vigorous shaking). In someother embodiments, the plurality of cells may be lysed usingultrasonication and/or by being passed through an 18-25 gauge syringeneedle at least once. In yet some other embodiments, the plurality ofcells may be lysed by being heated to about 70-90° C. For example, theplurality of cells may be lysed by being heated to about 70-90° C. forabout one or more hours. The cDNAs may then be isolated from the lysedcells. In some embodiments, RNase H may be added to the cDNA to removeRNA. The methods may further comprise ligating at least two of thenucleic acid tags that are bound to the released cDNAs. In some otherembodiments, the methods of labeling nucleic acids in the first cell maycomprise ligating at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, etc. of thenucleic acid tags that are bound to the cDNAs.

In various embodiments, the methods of labeling nucleic acids in thefirst cell may comprise removing one or more unbound nucleic acid tags(e.g., washing the plurality of cells). For example, the methods maycomprise removing a portion, a majority, or substantially all of theunbound nucleic acid tags. Unbound nucleic acid tags may be removed suchthat further rounds of the disclosed methods are not contaminated withone or more unbound nucleic acid tags from a previous round of a givenmethod. In some embodiments, unbound nucleic acid tags may be removedvia centrifugation. For example, the plurality of cells can becentrifuged such that a pellet of cells is formed at the bottom of acentrifuge tube. The supernatant (i.e., liquid containing the unboundnucleic acid tags) can be removed from the centrifuged cells. The cellsmay then be resuspended in a buffer (e.g., a fresh buffer that is freeor substantially free of unbound nucleic acid tags). In another example,the plurality of cells may be coupled or linked to magnetic beads thatare coated with an antibody that is configured to bind the cellmembrane. The plurality of cells can then be pelleted using a magnet todraw them to one side of the reaction vessel. In some other embodiments,the plurality of cells may be placed in a cell strainer (e.g., aPLURISTRAINER® cell strainer) and washed with a wash buffer. Forexample, the plurality of cells may remain in the cell strainer whilethe wash buffer passes through the cell strainer. Wash buffer mayinclude a surfactant, a detergent, and/or about 5-60% formamide.

As discussed above, the plurality of cells can be repooled and themethod can be repeated any number of times, adding more tags to thecDNAs creating a set of nucleic acid tags that can act as a barcode. Asmore and more rounds are added, the number of paths that a cell can takeincreases and consequently the number of possible barcodes that can becreated also increases. Given enough rounds and divisions, the number ofpossible barcodes will be much higher than the number of cells,resulting in each cell likely having a unique barcode. For example, ifthe division took place in a 96-well plate, after 4 divisions therewould be 96⁴=84,934,656 possible barcodes.

In some embodiments, the reverse transcription primer may be configuredto reverse transcribe all, or substantially all, RNA in a cell (e.g., arandom hexamer with a 5′ overhang). In some other embodiments, thereverse transcription primer may be configured to reverse transcribe RNAhaving a poly(A) tail (e.g., a poly(dT) primer, such as a dT(15) primer,with a 5′ overhang). In yet some other embodiments, the reversetranscription primer may be configured to reverse transcribepredetermined RNAs (e.g., a transcript-specific primer). For example,the reverse transcription primer may be configured to barcode specifictranscripts such that fewer transcripts may be profiled per cell, butsuch that each of the transcripts may be profiled over a greater numberof cells.

FIG. 2 illustrates the formation of cDNA by in situ reversetranscription. Panel A depicts a cell that is fixed and permeabilized.Panel B depicts addition of a poly(T) primer, as discussed above, whichcan template the reverse transcription of polyadenylated transcripts.Panel C depicts addition of a random hexamer, as discussed above, whichcan template the reverse transcription of substantially any transcript.Panel D depicts the addition of a primer that is designed to target aspecific transcript, as discussed above, such that only a subset oftranscripts may be amplified. Panel E depicts the cell of Panel A afterreverse transcription, illustrating a cDNA hybridized to an RNA.

Reverse transcription may be conducted or performed on the plurality ofcells. In certain embodiments, reverse transcription may be conducted ona fixed and/or permeabilized plurality of cells. In some embodiments,M-MuLV reverse transcriptase (ENZYMATICS™) may be used in the reversetranscription. Any suitable method of reverse transcription is withinthe scope of this disclosure. For example, a reverse transcription mixmay include a reverse transcription primer including a 5′ overhang andthe reverse transcription primer may be configured to initiate reversetranscription and/or to act as a binding sequence for nucleic acid tags.In some other embodiments, a portion of a reverse transcription primerthat is configured to bind to RNA and/or initiate reverse transcriptionmay comprise one or more of the following: a random hexamer, a septamer,an octomer, a nonamer, a decamer, a poly(T) stretch of nucleotides,and/or one or more gene specific primers.

Another aspect of the disclosure relates to methods of uniquely labelingmolecules within a cell or within a plurality of cells. In someembodiments, the method may comprise: (a) binding an adapter sequence,or universal adapter, to molecules within the plurality of cells; (b)dividing the plurality of cells into at least two primary aliquots,wherein the at least two primary aliquots comprise at least a firstprimary aliquot and a second primary aliquot; (c) providing primarynucleic acid tags to the at least two primary aliquots, wherein theprimary nucleic acid tags provided to the first primary aliquot aredifferent from the primary nucleic acid tags provided to the secondprimary aliquot; (d) binding the adapter sequences within each of the atleast two primary aliquots with the provided primary nucleic acid tags;(e) combining the at least two primary aliquots; (f) dividing thecombined primary aliquots into at least two secondary aliquots, the atleast two secondary aliquots comprising at least a first secondaryaliquot and a second secondary aliquot; (g) providing secondary nucleicacid tags to the at least two secondary aliquots, wherein the secondarynucleic acid tags provided to the first secondary aliquot are differentfrom the secondary nucleic acid tags provided to the second secondaryaliquot; and (h) binding the molecules within each of the at least twosecondary aliquots with the provided secondary nucleic acid tags.

In certain embodiments, the method may further comprise step (i), i.e.,repeating steps (e), (f), (g), and (h) with subsequent aliquots. Step(i) can be repeated a number of times sufficient to generate a uniqueseries of nucleic acid tags for the molecules in a single cell. Invarious embodiments, the number of times may be selected from 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,etc. In certain other embodiments, step (i) may be repeated anothersuitable number of times.

In some embodiments, the molecules may be disposed within the cell orwithin the plurality of cells. In some other embodiments, the moleculesmay be coupled to the cell or to the plurality of cells. For example,the molecules may be cell-surface molecules. In yet some otherembodiments, the molecules may be disposed within and/or coupled to thecell or the plurality of cells.

As discussed above, the method may comprise fixing and/or permeabilizingthe plurality of cells prior to step (a). In various embodiments, eachof the nucleic acid tags may comprise a first strand. The first strandmay comprise a barcode sequence including a 3′ end and a 5′ end. Thefirst strand may further comprise a 3′ hybridization sequence and a 5′hybridization sequence flanking the 3′ end and the 5′ end of the barcodesequence, respectively. In some embodiments, each of the nucleic acidtags may comprise a second strand. The second strand may comprise afirst portion complementary to at least one of the 5′ hybridizationsequence and the adapter sequence and a second portion complementary tothe 3′ hybridization sequence.

In certain embodiments, the molecules are macromolecules. In variousembodiments, the molecules are selected from at least one of RNA, cDNA,DNA, protein, peptides, and/or antigens.

In some embodiments, the molecules are RNA and the adapter sequence maybe single-stranded. Furthermore, step (a) may comprise one of ligating a5′ end of the single-stranded adapter sequence to a 3′ end of the RNAand/or ligating a 3′ end of the single-stranded adapter sequence to a 5′end of the RNA. In some other embodiments, the molecules are RNA andstep (a) may comprise hybridizing the adapter sequence to the RNA.

Methods related to binding or coupling an adapter sequence to an RNA canbe used, for example, in RNA transcriptome sequencing, ribosomeprofiling, small RNA sequencing, non-coding RNA sequencing, and/or RNAstructure profiling. In some embodiments, the plurality of cells may befixed and/or permeabilized. The 5′ end of a single-stranded adaptersequence may be ligated to the 3′ end of an RNA (see FIGS. 3A and 3B).In certain embodiments, the ligation may be conducted or performed by T4RNA Ligase 1. In certain other embodiments, the ligation may beconducted by T4 RNA Ligase 1 with a single-stranded adapter sequenceincluding a 5′ phosphate. In various embodiments, the ligation may beconducted by THERMOSTABLE 5′ APPDNA/RNA LIGASE™ (NEW ENGLAND BIOLABS®).In various other embodiments, the ligation may be conducted byTHERMOSTABLE 5′ APPDNA/RNA LIGASE™ with a 5′ pre-adenylatedsingle-stranded adapter sequence. Other suitable ligases and adaptersequences are also within the scope of this disclosure.

In some embodiments, the RNA can be labeled with adapter sequence usinghybridization, for example, via Watson-Crick base-pairing (see FIG. 4 ).After the labeling steps and/or cell lysis, as discussed above, theadapter sequence may be configured to prime reverse transcription toform or generate cDNA (see FIG. 5 ).

The 3′ end of a single-stranded adapter sequence may be ligated to the5′ end of an RNA. In certain embodiments, the ligation may be conductedor performed by T4 RNA Ligase 1. In certain other embodiments, theligation may be conducted by T4 RNA Ligase 1 with an RNA including a 5′phosphate. In various embodiments, the ligation may be conducted byTHERMOSTABLE 5′ APPDNA/RNA LIGASE™ (NEW ENGLAND BIOLABS®). In variousother embodiments, the ligation may be conducted by THERMOSTABLE 5′APPDNA/RNA LIGASE™ with a 5′ pre-adenylated RNA. As stated above, othersuitable ligases and adapter sequences are also within the scope of thisdisclosure.

In some embodiments, the molecules may be cDNA. Methods related tobinding or coupling an adapter sequence to a cDNA can be used, forexample, in RNA transcriptome sequencing. In certain embodiments, theplurality of cells may be fixed and/or permeabilized. Reversetranscription may be performed on the plurality of fixed and/orpermeabilized cells with a primer that includes the adapter sequence onthe 5′ end. As discussed above, the 3′ end of the primer may begene-specific, a random hexamer, or a poly(T) sequence. The resultingcDNA may include the adapter sequence on its 5′ end (see FIG. 5 ).

In some embodiments, wherein the molecules are DNA (e.g., genomic DNA),the method may further comprise digesting the DNA with a restrictionenzyme prior to step (a). Furthermore, step (a) may comprise ligatingthe adapter sequence to the digested DNA.

Methods related to binding or coupling an adapter sequence to a DNA maybe used, for example, in whole genome sequencing, targeted genomesequencing, DNase-Seq, ChIP-sequencing, and/or ATAC-seq. In certainembodiments, one or more restriction enzymes may be used to digest DNAinto at least one of blunt end fragments and/or fragments havingoverhang sequences. A partial double-stranded sequence with thesingle-stranded universal adapter or adapter sequence protruding on oneend can be ligated to the digested genomic DNA. For example, a partialdouble-stranded sequence with the single-stranded adapter sequencehaving an overhang, wherein the overhang is compatible with the overhanggenerated by the one or more restriction enzymes, may be ligated to thedigested genomic DNA.

In various embodiments, adapter sequences can be integrated (e.g.,directly integrated) into genomic DNA using Tn5 transposase and thetransposase can be released to expose the adapter sequences by additionof sodium dodecyl sulfate (SDS). Other transposases and methods ofintegrating the adapter sequences into genomic DNA are also within thescope of this disclosure.

In certain embodiments, the molecules are protein, peptide, and/orantigen, and the adapter sequence may be bound to a unique identifiersequence (e.g., comprising nucleic acids) that is coupled to anantibody. The unique identifier sequence may be configured to uniquelyidentify the antibody to which the unique identifier sequence is bound.Furthermore, step (a) may comprise binding the antibodies, whichcomprise each of the adapter sequence and the unique identifiersequence, to the protein, peptide, and/or antigen. In certain otherembodiments, the molecules are protein, peptide, and/or antigen, and theadapter sequence may be integrated in an aptamer. Furthermore, step (a)may comprise binding the aptamer to the protein, peptide, and/orantigen.

Methods related to binding or coupling an adapter sequence to a protein,a peptide, and/or an antigen may be used, for example, in proteinquantification, peptide quantification, and/or antigen quantification.In various embodiments, the adapter sequence can be attached (e.g.,chemically attached) to an antibody. For example, the adapter sequencecan be attached to an antibody using chemistry known to the skilledartisan for mediating DNA-protein bonds. Antibodies for differentproteins can be labeled with nucleic acid sequences or strands thatinclude a unique identifier sequence in addition to the adaptersequence. The antibody, or set of antibodies, may then be used in animmunostaining experiment to label a protein, or set of proteins, infixed and/or permeabilized cells or tissue (see FIG. 6 ). Subsequently,the cells may undergo a labeling or barcoding procedure as disclosedherein.

In some embodiments, the nucleic acid sequences (e.g., the DNAmolecules) attached or bound to the antibodies can be released from theantibodies and/or adapter sequences. A sequencing reaction can reveal aunique identifier sequence associated with a given protein as well asthe label or barcode associated with a unique cell or cells. In certainembodiments, such a method may reveal or identify the number and/or typeof proteins present in one or more cells.

In various embodiments, a DNA aptamer and/or an RNA aptamer can be usedinstead of, or in addition to, a nucleic acid-modified (or DNA-modified)antibody as described above (see FIG. 7 ). The adapter sequence (andtarget protein-specific antibody) may be integrated (e.g., directlyintegrated) into the sequence of a given aptamer.

Another aspect of the disclosure relates to methods of barcoding nucleicacids within a cell. In some embodiments, the methods of barcodingnucleic acids within a cell may comprise: (a) generating cDNAs within aplurality of cells by reverse transcribing RNAs using a reversetranscription primer comprising a 5′ overhang sequence; (b) dividing theplurality of cells into at least two aliquots; (c) providing a pluralityof nucleic acid tags to each of the at least two aliquots, wherein eachbarcode sequence of the plurality of nucleic acid tags introduced into agiven aliquot is the same, and wherein a different barcode sequence isintroduced into each aliquot; (d) binding at least one of the cDNAs ineach of the at least two aliquots to the nucleic acid tags; (e)combining the at least two aliquots; and (f) repeating steps (b), (c),(d), and (e) at least once with the combined aliquot.

In certain embodiments, each nucleic acid tag may comprise a firststrand comprising a 3′ hybridization sequence extending from a 3′ end ofa barcode sequence and a 5′ hybridization sequence extending from a 5′end of the barcode sequence. Each nucleic acid tag may also comprise asecond strand comprising an overhang sequence, wherein the overhangsequence comprises (i) a first portion complementary to at least one ofthe 5′ hybridization sequence and the 5′ overhang sequence and (ii) asecond portion complementary to the 3′ hybridization sequence.

FIG. 8 depicts dividing, tagging, and pooling of cells, according to anembodiment of the present disclosure. Cells that have been reversetranscribed can be divided between reaction vessels or wells. In FIG. 8, 4 wells are shown. As discussed above, however, any suitable number ofreaction vessels or wells may be used. One cell is highlighted to showits path through the process. As depicted, the highlighted cell firstends up in well ‘a’, wherein it is the 1^(st) tag added to it thathybridizes to the overhang of all the cDNA transcripts (shown in thebox). The tag carries a unique barcode region ‘a’, identifying the wellthat the cell was in. After hybridization, all cells are washed toremove excess tags, regrouped, and then split again between the samenumber of wells. The highlighted cell then ends up in well ‘c’ and has a2^(nd) tag added to it identifying the well it was in. After the secondround, the cells could have taken 4²=16 possible paths through thetubes. The process can be repeated, adding more tags to the cDNAtranscripts and increasing the number of possible paths the cells cantake. FIGS. 9A and 9B depict two exemplary workflows, according toembodiments of the present disclosure.

Another aspect of the disclosure relates to kits for labeling nucleicacids within at least a first cell. In some embodiments, the kit maycomprise at least one reverse transcription primer comprising a 5′overhang sequence. The kit may also comprise a plurality of firstnucleic acid tags. Each first nucleic acid tag may comprise a firststrand. The first strand may include a 3′ hybridization sequenceextending from a 3′ end of a first labeling sequence and a 5′hybridization sequence extending from a 5′ end of the first labelingsequence. Each first nucleic acid tag may further comprise a secondstrand. The second strand may include an overhang sequence, wherein theoverhang sequence may comprise (i) a first portion complementary to atleast one of the 5′ hybridization sequence and the 5′ overhang sequenceof the reverse transcription primer and (ii) a second portioncomplementary to the 3′ hybridization sequence.

The kit may further comprise a plurality of second nucleic acid tags.Each second nucleic acid tag may comprise a first strand. The firststrand may include a 3′ hybridization sequence extending from a 3′ endof a second labeling sequence and a 5′ hybridization sequence extendingfrom a 5′ end of the second labeling sequence. Each second nucleic acidtag may further comprise a second strand. The second strand may comprisean overhang sequence, wherein the overhang sequence may comprise (i) afirst portion complementary to at least one of the 5′ hybridizationsequence and the 5′ overhang sequence of the reverse transcriptionprimer and (ii) a second portion complementary to the 3′ hybridizationsequence. In some embodiments, the first labeling sequence may bedifferent from the second labeling sequence.

In some embodiments, the kit may also comprise one or more additionalpluralities of nucleic acid tags. Each nucleic acid tag of the one ormore additional pluralities of nucleic acid tags may comprise a firststrand. The first strand may include a 3′ hybridization sequenceextending from a 3′ end of a labeling sequence and a 5′ hybridizationsequence extending from a 5′ end of the labeling sequence. Each nucleicacid tag of the one or more additional pluralities of nucleic acid tagsmay also comprise a second strand. The second strand may include anoverhang sequence, wherein the overhang sequence comprises (i) a firstportion complementary to at least one of the 5′ hybridization sequenceand the 5′ overhang sequence of the reverse transcription primer and(ii) a second portion complementary to the 3′ hybridization sequence. Insome embodiments, the labeling sequence may be different in each givenadditional plurality of nucleic acid tags.

In various embodiments, the kit may further comprise at least one of areverse transcriptase, a fixation agent, a permeabilization agent, aligation agent, and/or a lysis agent.

Another aspect of the disclosure relates to kits for labeling moleculeswithin at least a first cell. For example, the kits as disclosed abovemay be adapted to label one or more of RNA, cDNA, DNA, protein,peptides, or antigens within at least a first cell.

As will be understood by one of ordinary skill in the art, eachembodiment disclosed herein can comprise, consist essentially of, orconsist of its particular stated element, step, ingredient, orcomponent. As used herein, the transition term “comprise” or “comprises”means includes, but is not limited to, and allows for the inclusion ofunspecified elements, steps, ingredients, or components, even in majoramounts. The transitional phrase “consisting of” excludes any element,step, ingredient or component not specified. The transition phrase“consisting essentially of” limits the scope of the embodiment to thespecified elements, steps, ingredients or components, and to those thatdo not materially affect the embodiment.

Unless otherwise indicated, all numbers expressing quantities ofingredients, properties such as molecular weight, reaction conditions,and so forth used in the specification and claims are to be understoodas being modified in all instances by the term “about.” Accordingly,unless indicated to the contrary, the numerical parameters set forth inthe specification and attached claims are approximations that may varydepending upon the desired properties sought to be obtained by thepresent disclosure. At the very least, and not as an attempt to limitthe application of the doctrine of equivalents to the scope of theclaims, each numerical parameter should at least be construed in lightof the number of reported significant digits and by applying ordinaryrounding techniques. When further clarity is required, the term “about”has the meaning reasonably ascribed to it by a person skilled in the artwhen used in conjunction with a stated numerical value or range, i.e.,denoting somewhat more or somewhat less than the stated value or range,to within a range of ±20% of the stated value; ±19% of the stated value;±18% of the stated value; ±17% of the stated value; ±16% of the statedvalue; ±15% of the stated value; ±14% of the stated value; ±13% of thestated value; ±12% of the stated value; ±11% of the stated value; ±10%of the stated value; ±9% of the stated value; ±8% of the stated value;±7% of the stated value; ±6% of the stated value; ±5% of the statedvalue; ±4% of the stated value; ±3% of the stated value; ±2% of thestated value; or ±1% of the stated value.

Notwithstanding that the numerical ranges and parameters setting forththe broad scope of the disclosure are approximations, the numericalvalues set forth in the specific examples are reported as precisely aspossible. Any numerical value, however, inherently contains certainerrors necessarily resulting from the standard deviation found in theirrespective testing measurements.

The terms “a,” “an,” “the” and similar referents used in the context ofdescribing the disclosure (especially in the context of the followingclaims) are to be construed to cover both the singular and the plural,unless otherwise indicated herein or clearly contradicted by context.Recitation of ranges of values herein is merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range. Unless otherwise indicated herein, eachindividual value is incorporated into the specification as if it wereindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein isintended merely to better illuminate the disclosure and does not pose alimitation on the scope of the disclosure otherwise claimed. No languagein the specification should be construed as indicating any non-claimedelement essential to the practice of the disclosure.

Groupings of alternative elements or embodiments of the disclosuredisclosed herein are not to be construed as limitations. Each groupmember may be referred to and claimed individually or in any combinationwith other members of the group or other elements found herein. It isanticipated that one or more members of a group may be included in, ordeleted from, a group for reasons of convenience and/or patentability.When any such inclusion or deletion occurs, the specification is deemedto contain the group as modified thus fulfilling the written descriptionof all Markush groups used in the appended claims.

Definitions and explanations used in the present disclosure are meantand intended to be controlling in any future construction unless clearlyand unambiguously modified in the following examples or when applicationof the meaning renders any construction meaningless or essentiallymeaningless in cases where the construction of the term would render itmeaningless or essentially meaningless, the definition should be takenfrom Webster's Dictionary, 3rd Edition or a dictionary known to those ofordinary skill in the art, such as the Oxford Dictionary of Biochemistryand Molecular Biology (Ed. Anthony Smith, Oxford University Press,Oxford, 2004).

EXAMPLES

The following examples are illustrative of disclosed methods andcompositions. In light of this disclosure, those of skill in the artwill recognize that variations of these examples and other examples ofthe disclosed methods and compositions would be possible without undueexperimentation.

Example 1—Fixation and Reverse Transcription

NIH/3T3 (mouse) and Hela-S3 (human) cells can be grown to confluence ontwo separate 10 cm cell culture plates. The cells can be rinsed twicewith 10 ml 1× phosphate buffered saline (PBS), 1 ml of 0.05% trypsin canbe added to each plate, and the plates can be incubated at 37° C. for 5minutes. The cells can be detached by tilting each plate at a 45° anglewhile pipetting trypsin across the plates, which can be continued untilall, or substantially all, of the cells are detached. Each cell line canbe transferred into its own 15 ml conical centrifuge tube (FALCON™). 2ml of Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovineserum (FBS) can be added to each tube. The number of cells in each tubecan be calculated (e.g., with a hemocytometer or on a flow cytometer).For example, 200 μl of the sample can be transferred from each tube intoseparate 1.7 ml microcentrifuge tubes (EPPENDORF®) and 100 μl of thesample can be run on an ACCURI™ Flow Cytometer to calculate the cellconcentration.

The same number of cells from each tube can be combined into a newsingle 15 ml conical centrifuge tube (FALCON™), using as many cells aspossible. A 5 minute spin can be conducted at 500×g in a 15 ml conicalcentrifuge tube (FALCON™). It may be helpful to use a bucket centrifugeso that the cells are pelleted at the bottom of the tube rather than onthe side of the tube. The liquid can be aspirated without disturbing thecell pellet and the cells can be resuspended in 500 μl of 4%formaldehyde. The cells can then be left at room temperature (i.e.,20-25° C.) for 10 minutes. 1.5 ml of 0.5% TRITON™ X-100 can be added tothe tube and mixed gently with a pipette. The tube can them be spun at500×g for 5 minutes. Again, the liquid can be aspirated withoutdisturbing the pellet and the pellet can be washed twice with 1 ml PBSwithout resuspending the pellet. If washing disturbs the pellet, thesecond wash can be skipped. The pellet can then be resuspended in 1 ml0.1 N HCl and incubated at room temperature for 5 minutes.

2 ml of Tris-HCl (pH 8.0) can be added to a new 15 ml conical centrifugetube (FALCON™). The fixed cells in HCl, from above, can be transferredto the tube with Tris-HCl so as to neutralize the HCl. The number ofcells in the tube can then be calculated as discussed above (e.g., witha hemocytometer or on a flow cytometer). The fixed cells in Tris-HCl canbe spun down at 500×g for 5 minutes and the liquid can be aspiratedwithout disturbing the pellet. The pellet can be washed twice with 1 mlRNase-free molecular grade water, without disturbing the pellet. Thecells can then be resuspended to a concentration of 2.5 million cells/ml(to do this, the concentration calculated before the last spin step canbe used).

A reverse transcription mix can be made (55 μl M-MuLV reversetranscriptase buffer (ENZYMATICS™), 55 μl M-MuLV reverse transcriptase(ENZYMATICS™), 5.5 μl dNTPs (25 mM per base), 3.44 μl RNase inhibitor(ENZYMATICS™, 40 units/μl), 210.4 μl nuclease-free water, and 2.75 μl RTPrimer (BC_0055, 100 μM)). In a well of a 24-well cell culture plate,300 μl of the reverse transcription mix can be combined with 200 μl ofthe fixed cells (˜500,000 cells) and mixed gently by pipetting. Themixture can then be incubated at room temperature for 10 minutes toallow the reverse transcription primer to anneal and the mixture canthen be incubated at 37° C. in a humidified incubator overnight (i.e.,˜16 hours).

A primer that can be used for reverse transcription (BC_0055) isdepicted in FIG. 10 . This is an anchored primer, designed to bind thestart of a poly(A) tail of a messenger RNA. The primer may besynthesized with all 4 bases at the 3′ end (N) and every base except Tat the second-most 3′ position (V). The primer can also include 15consecutive dTs. In some embodiments, the primer may include more than15 dTs. In some other embodiments, the primer may include fewer than 15dTs. In embodiments wherein the primer includes fewer than 15 dTs, themelting temperature of the primer may be lowered. The domain s0 may nothybridize to messenger RNAs, but may instead provide an accessiblebinding domain for a linker oligo. The primer also includes a 5′phosphate that can allow ligation of the primer to another oligo by T4DNA ligase.

Example 2—Preparation of Barcodes

The barcodes were ordered in 96-well plates at 100 μM concentrations.Each barcode was annealed with its corresponding linker oligo (see FIGS.10-12 ).

FIG. 11 depicts an annealed, first-round barcode oligo. 96 first-roundbarcode oligos with unique sequences in domain i8a were used. In thefirst round, the unique sequence in domain i8a is the region of thesequence that is used as a barcode. By varying 8 nucleotides, there are65,536 possible unique sequences. In some embodiments, more than 8nucleotides may be present in domain i8a. In some other embodiments,fewer than 8 nucleotides may be present in domain i8a. The first-roundbarcodes were preannealed to a linker strand (BC_0056) throughcomplementary sequences in domain s1. The linker strand can includecomplementary sequence to part of the reverse transcription primer(domain s0) that can allow it to hybridize and bring the 3′ end of thefirst-round barcodes in close proximity to the 5′ end of the reversetranscription primer. The phosphate of the reverse transcription primercan then be ligated to the 3′ end of the first-round barcodes by T4 DNAligase. The domain s2 can provide an accessible binding domain for alinker oligo to be used in another round of barcoding. The first-roundbarcode oligos can include a 5′ phosphate that can allow ligation to the3′ end of another oligo by T4 DNA ligase.

FIG. 12 depicts an annealed, second-round barcode oligo. 96 second-roundbarcode oligos with unique sequences in domain i8b were used. In thesecond round, the unique sequence in domain i8b is the region of thesequence that is used as a barcode. By varying 8 nucleotides, there are65,536 possible unique sequences. In some embodiments, more than 8nucleotides may be present in domain i8b. In some embodiments, less than8 nucleotides may be present in domain i8b. The second-round barcodescan be preannealed to a linker strand (BC_0058) through complementarysequences in domain s3. The linker strand can include complementarysequence to part of the first-round barcode oligo (domain s2) that canallow it to hybridize and bring the 3′ end of the first-round barcodesin close proximity to the 5′ end of the second-round barcode oligo. Thephosphate of the first-round barcode oligo can then be ligated to the 3′end of the second-round barcodes by T4 DNA ligase. The domain s4 canprovide an accessible binding domain for a linker oligo to be used inanother round of barcoding. The second-round barcode oligos can includea 5′ phosphate that can allow ligation to the 3′ end of another oligo byT4 DNA ligase.

FIG. 13 depicts an annealed, third-round barcode oligo. 96 third-roundbarcode oligos with unique sequences in domain i8c were used. In thethird round, the unique sequence in domain i8c is the region of thesequence that is used as a barcode. By varying 8 nucleotides, there are65,536 possible unique sequences. In some embodiments, more than 8nucleotides may be present in domain i8c. In some other embodiments,less than 8 nucleotides may be present in domain i8c. The third round ofbarcodes can be preannealed to a linker strand (BC_0060) throughcomplementary sequences in domain s5. The linker strand can includecomplementary sequence to part of the second-round barcode oligo (domains4) that can allow it to hybridize and bring the 3′ end of thesecond-round barcodes in close proximity to the 5′ end of thethird-round barcode oligo. The phosphate of the second-round barcodeoligo can then be ligated to the 3′ end of the third-round barcodes byT4 DNA ligase. The third-round barcode oligos can be synthesized withunique molecular identifiers (UMI; see Islam, et. al. Nature Methods,2014) consisting of 10 random nucleotides (domain UMI: NNNNNNNNNN). Dueto PCR amplification bias, multiple sequencing reads can originate fromthe cDNA. Using a UMI, each cDNA may be counted only once. Thethird-round barcodes can also include a domain corresponding to part ofthe ILLUMINA® TruSeq adapter. The third-round barcodes can besynthesized with a biotin molecule at the 5′ end so that fully barcodedcDNA can be isolated with streptavidin coated magnetic beads.

Starting from a 100 μM stock of each barcode oligo (i.e., in 96-wellplates, one for each round), 11 μl of barcode oligo were transferred to96-well PCR plates. To the plate with the round 1 barcodes, 9 μl ofBC_0056 (100 μM stock) were added to each well. To the plate with theround 2 barcodes, 9 μl of BC_0058 (100 μM stock) were added to eachwell. To the plate with the round 3 barcodes, 9 μl of BC_0060 (100 μMstock) were added to each well. Each plate was then placed in athermocycler, with the following program, to anneal the barcodes withthe corresponding linker oligo: heat to 90° C., reduce heat 0.1°C./second, and stop when the temperature reaches 25° C. 2.2 μl weretransferred from each well having the round 1 barcodes into a new96-well plate (referred to as plate L1). 3.8 μl were transferred fromeach well with the round 2 barcodes into a new 96-well plate (referredto as plate L2). 6.1 μl were transferred from each well with the round 3barcodes into a new 96-well plate (referred to as plate L3).

Example 3—Preparation of Ligation Stop Oligos

After each round of ligation, the ligation can be stopped by adding anexcess of oligo that is complementary to the linker strands (see FIG. 14). To stop each barcode ligation, oligo strands that are fullycomplementary to the linker oligos can be added. These oligos can bindthe linker strands attached to unligated barcodes and displace theunligated barcodes through a strand displacement reaction. The unligatedbarcodes can then be completely single-stranded. As T4 DNA ligase isunable to ligate single-stranded DNA to other single-stranded DNA, theligation reaction will stop progressing. To ensure that all linkeroligos are bound by the complementary oligos, a molar excess of thecomplementary oligos (relative to the linker oligos) is added. To stopthe first-round ligation, BC_0064 (complementary to BC_0056) is added.To stop the second-round ligation, BC_0065 (complementary to BC_0058) isadded. To stop the third-round ligation, BC_0066 (complementary toBC_0060) is added.

Dilutions can be prepared for each stop ligation strand (BC_0064,BC_0065, BC_0066) as follows: 264 μl stop ligation strand (BC_0064,BC_0065, BC_0066), 300 μl 10× T4 DNA Ligase Buffer, and 636 μlnuclease-free water.

Example 4—Ligation of Barcodes to cDNA

5 μl 10% TRITON™ X-100 can be added to the reverse transcriptionreaction (to a final concentration of 0.1%) in the above-described24-well plate. The reverse transcription (RT) reaction with cells can betransferred to a 15 ml conical centrifuge tube (FALCON™). The RTreactions can be spun for 10 minutes at 500×g and resuspended in 2 mlnuclease-free water. The cells can be combined with ligase mix (600 μl10× T4 ligase buffer, 2040 μl of nuclease-free water, all of theresuspended cells (2000 μl), 100 μl of T4 DNA Ligase (NEW ENGLANDBIOLABS®, 400,000 units/ml), and 60 μl of 10% TRITON™ X-100) in adisposable pipetting reservoir (10 ml)). The cells and ligase mix can bemixed by gently tilting the reservoir back and forth several times.Using a multichannel pipette, 40 μl of the cells in the ligase mix canbe added to each well of annealed round 1 barcodes (plate L1). Each wellcan be mixed by pipetting up and down gently 2-3 times. The cells in theligase mix can be incubated at 37° C. for 60 minutes.

10 μl of the diluted BC_0064 can be added to each well to stop theligation. The samples can then be incubated at 37° C. for 30 minutes.All of the cells can be collected in a new disposable pipettingreservoir (10 ml). The cells can be passed through a 40 μM strainer intoa new disposable pipetting reservoir (10 ml) using a 1 ml pipette. 100μl of T4 DNA ligase (NEW ENGLAND BIOLABS®, 400,000 units/ml) can beadded to the cells in reservoir. The cells and ligase mix can be mixedby gently tilting the reservoir back and forth several times and using amultichannel pipette, 40 μl of the cells in the ligase mix can be addedto each well of annealed round 2 barcodes (plate L2). Each well can bemixed by pipetting up and down gently 2-3 times and the samples can thenbe incubated at 37° C. for 60 minutes.

10 μl of the diluted BC_0065 can be added to each well to stop theligation. The samples can be incubated at 37° C. for 30 minutes and thecells can then be collected in a new disposable pipetting reservoir (10ml). The cells can be passed through a 40 μM strainer into a newdisposable pipetting reservoir (10 ml) using a 1 ml pipette. 100 μl ofT4 DNA ligase (NEW ENGLAND BIOLABS®, 400,000 units/ml) can be added tothe cells in the reservoir. The cells and ligase mix can be mixed bygently tilting the reservoir back and forth several times. Using amultichannel pipette, 40 μl of the cells in the ligase mix can be addedto each well of annealed round 3 barcodes (plate L3). Each well can thenbe mixed by pipetting up and down gently 2-3 times and the samples canbe incubated at 37° C. for 60 minutes.

10 μl of the diluted BC_0066 can be added to each well to stop theligation. The samples can be incubated at 37° C. for 30 minutes. All thecells can be collected in a new disposable pipetting reservoir (10 ml).The cells can be transferred to a 15 ml conical centrifuge tube(FALCON™) and the tube can be filled with wash buffer (nuclease-freewater, 0.05% Tween 20, and 25% formamide) to 15 ml. The samples can beincubated for 15 minutes at room temperature. The cells can then bepelleted at 500×g for 10 minutes and the liquid can be removed withoutdisturbing the pellet. Each tube of cells can be resuspended in 100 μlPBS and the cells can be counted (e.g., on a hemocytometer or on a flowcytometer). In one example, 57,000 cells were retained. The number ofcells to be sequenced can be chosen. In one example, the cells weresplit into 25 cell, 250 cell, 2,500 cell, and 25,000 cell aliquots. 300μl of lysis buffer (10 mM NaF, 1 mM Na₃VO₄, 0.5% DOC buffer, and 0.5%TRITON™ X-100) can be added to each of the cell aliquots and each of thecell aliquots can be passed through a 25 gauge needle eight times.

Example 5—Binding Barcoded cDNA to Streptavidin Coated Beads

First, DYNABEADS® MYONE™ Streptavidin Cl beads can be resuspended. 20 μlof resuspended DYNABEADS® MYONE™ Streptavidin Cl beads (for each aliquotof cells) can be added to a 1.7 ml microcentrifuge tube (EPPENDORF®).The beads can be washed 3 times with 1× phosphate buffered saline Tween20 (PBST) and resuspended in 20 μl PBST. 900 μl PBST can be added to thecell aliquot and 20 μl of washed Cl beads can be added to the aliquot oflysed cells. The samples can be placed on a gentle roller for 15 minutesat room temperature and then washed 3 times with 800 μl PBST using amagnetic tube rack (EPPENDORF®). The beads can then be resuspended in100 μl PBS.

Example 6—RNase Treatment of Beads

A microcentrifuge tube (EPPENDORF®) comprising a sample can be placedagainst a magnetic tube rack (EPPENDORF®) for 2 minutes and then theliquid can be aspirated. The beads can be resuspended in an RNasereaction (3 μl RNase Mix (ROCHE™), 1 μl RNase H (NEW ENGLAND BIOLABS®),5 μl RNase H 10× Buffer (NEW ENGLAND BIOLABS®), and 41 μl nuclease-freewater). The sample can be incubated at 37° C. for 1 hour, removed from37° C., and placed against a magnetic tube rack (EPPENDORF®) for 2minutes. The sample can be washed with 750 μl of nuclease-freewater+0.01% Tween 20 (H₂O-T), without resuspending the beads and keepingthe tube disposed against the magnetic tube rack. The liquid can then beaspirated. The sample can be washed with 750 μl H₂O-T withoutresuspending the beads and while keeping the tube disposed against themagnetic tube rack. Next, the liquid can be aspirated while keeping thetube disposed against the magnetic tube rack. The tube can then beremoved from the magnetic tube rack and the sample can be resuspended in40 μl of nuclease-free water.

Example 7-3′ Adapter Ligation

With reference to FIG. 15 , to facilitate PCR amplification, asingle-stranded DNA adapter oligo (BC_0047) can be ligated to the 3′ endof cDNA. To prevent concatemers of the adapter oligo, dideoxycytidine(ddC) can be included at the 3′ end of the adapter oligo. BC_0047 wasgenerated with a phosphate at the 5′ end and ddC at the 3′ end. Severalenzymes are capable of ligating single-stranded oligo to the 3′ end ofsingle-stranded DNA. Herein, T4 RNA ligase 1 (NEW ENGLAND BIOLABS®) wasused. Thermostable 5′ AppDNA/RNA Ligase (NEW ENGLAND BIOLABS®) can alsobe used with a preadenylated adaptor oligo.

Specifically, 20 μl of the RNase-treated beads can be added to a singlePCR tube. 80 μl of ligase mix (5 μl T4 RNA Ligase 1 (NEW ENGLANDBIOLABS®), 10 μl 10× T4 RNA ligase buffer, 5 μl BC_0047 oligo at 50 μM,50 μl 50% PEG 8000, and 10 μl 10 mM ATP) can be added to the 20 μl ofbeads in the PCR tube. 50 μl of the ligase mixed with the beads can betransferred into a new PCR tube to prevent too many beads from settlingto the bottom of a single tube and the sample can be incubated at 25° C.for 16 hours.

Example 8—Generating ILLUMINA® Compatible Sequencing Products

Ligation reactions from both PCR tubes can be combined into a single 1.7ml microcentrifuge tube (EPPENDORF®). 750 μl of H₂O-T can be added toeach sample. Each of the tubes can be placed on a magnetic tube rack(EPPENDORF®) for 2 minutes, the liquid can be aspirated, and the samplescan be resuspended in 40 μl water. The samples can be transferred to PCRtubes. 60 μl of PCR mix can be added to each tube (50 μl 2× PHUSION® DNAPolymerase Master Mix (THERMO FISHER™ Scientific), 5 μl BC_0051 (10 μM),and 5 μl BC_0062 (10 μM)). 10 cycles of PCR can be run (98° C. for 3minutes, repeat 10 times (98° C. for 10 seconds, 65° C. for 15 seconds,and 72° C. for 60 seconds), and 72° C. for 5 minutes). FIG. 16 depictsthe PCR product. After the 3′ adapter oligo (BC_0047) has been ligatedto barcoded cDNA, the cDNA can be amplified using PCR. As shown in FIG.16 , the primers BC_0051 and BC_0062 were used.

The PCR samples from the previous step can be procured and the magneticbeads can be displaced to the bottom of each tube with a magnet. 90 μlof PCR reaction can be transferred to a new 1.7 ml without transferringany of the magnetic beads. 10 μl of nuclease-free water can be added toeach of the 1.7 ml tubes to a total volume of 100 μl. 60 μl of AMPURE™beads can be added to the 100 μl of PCR reaction (0.6×SPRI) and boundfor 5 minutes. The tubes can be placed against a magnet for 2 minutesand the samples can be washed with 200 μl of 70% ethanol (30 secondwait) without resuspending the beads. The samples can be washed againwith 200 μl of 70% ethanol (30 second wait) without resuspending thebeads and then the samples can be air dried for 5-10 minutes until theethanol has evaporated.

Each of the samples can be resuspended in 40 μl of nuclease-free water.The tubes can be placed against a magnetic rack for 2 minutes. While themicrocentrifuge tubes (EPPENDORF®) are still disposed against themagnetic rack, 38 μl of solution can be transferred to a new 1.7 mltube, without transferring beads. 62 μl of nuclease-free water can beadded to the samples to a total volume of 100 μl. 60 μl of AMPURE™ beadscan then be added to 100 μl of the PCR reaction (0.6×SPRI) and bound for5 minutes. The tubes can be placed against a magnet for 2 minutes andthen the samples can be washed with 200 μl of 70% ethanol (30 secondwait) without resuspending the beads. The samples can be washed againwith 200 μl 70% ethanol (30 second wait) without resuspending the beadsand then the samples can be air dried for 5-10 minutes until the ethanolhas evaporated.

The samples can be resuspended in 40 μl of nuclease-free water and eachtube can be placed against a magnetic rack for 2 minutes. While the tubeis still disposed against the magnetic rack, 38 μl of solution to a new1.7 ml tube, without transferring any beads. 20 μl of the 38 μl elutioncan be added to an optical PCR tube. Furthermore, a PCR mix can be addedto the tube (25 μl PHUSION® DNA Polymerase Master Mix (THERMO FISHER™Scientific), 2.5 μl BC_0027 (10 μM), 2.5 μl BC_0063 (10 μM), and 2.5 μl20× EVAGREEN® (Biotium)). Following the PCR depicted in FIG. 16 , thefull ILLUMINA® adapter sequences can be introduced through another roundof PCR. As depicted in FIG. 17 , BC_0027 includes the flow cell bindingsequence and the binding site for the TRUSEQ™ read 1 primer. BC_0063includes the flow cell binding sequence and the TruSeq multiplex read 2and index binding sequence. There is also a region for the sample index,which is GATCTG in this example.

The above samples can be run on a qPCR machine with the followingcycling conditions: 1) 98° C. for 3 minutes, 2) 98° C. for 10 seconds,3) 65° C. for 15 seconds, 4) 72° C. for 60 seconds, and 5) repeat steps2-4 (e.g., 10-40 times, depending on when fluorescence stops increasingexponentially). The tube can be transferred to a thermocycler set to 72°C. for 5 minutes. The qPCR reaction can be run on a 1.5% agarose gel for40 minutes and a 450-550 bp band can be removed and gel extracted(QIAQUICK® Gel Extraction Kit). The products can be sequenced on anILLUMINA® MISEQ™ using paired end sequencing. The sequencing primers canbe the standard TRUSEQ™ multiplex primers. Read 1 can sequence the cDNAsequence, while read 2 can cover the unique molecular identifier as wellas the 3 barcode sequences (8 nucleotides each). Index read 1 can beused to sequence sample barcodes, so multiple samples may be sequencedtogether.

Example 9—Data Analysis

Sequencing reads were grouped by cell barcodes (three barcodes of eightnucleotides each, 96×96×96=884,736 total combinations). Each barcodecombination should correspond to the cDNA from a single cell. Only readswith valid barcodes were retained. The sequencing reads with eachbarcode combination were aligned to both the human genome and the mousegenome. Reads aligning to both genomes were discarded. Multiple readswith the same unique molecular identifier were counted as a single read.Reads with unique molecular identifiers with two or less mismatches wereassumed to be generated by sequencing errors and were counted as asingle read. For each unique barcode combination the number of readsaligning to the human genome (x-axis) and the mouse genome (y-axis) wereplotted (see FIG. 18 ). As each cell is either mouse or human, it shouldideally include only one type of RNA. So an ideal plot would have everypoint along the x- or y-axis. The fact that most points in the plot ofFIG. 18 are near an axis indicates that the method is viable.

Each point in the plot corresponds to cDNA with the same combination ofbarcodes and should represent the cDNA from a single cell. For eachpoint, the number of reads that map uniquely to the mouse genome areplotted on the y-axis, while the number of reads that map uniquely tothe human genome are plotted on the x-axis. If cDNAs with a specificcombination of barcodes came from a single cell, all of the cDNA withthe specific combination of barcodes should map completely to the humangenome or completely to the mouse genome. As stated above, the fact thatmost barcode combinations map close to either the x-axis (human cells)or the y-axis (mouse cells) indicates that the method can indeed producesingle-cell RNA sequencing data.

Certain embodiments of this disclosure are described herein, includingthe best mode known to the inventors for carrying out the disclosure. Ofcourse, variations on these described embodiments will become apparentto those of ordinary skill in the art upon reading the foregoingdescription. The applicants expect skilled artisans to employ suchvariations as appropriate, and the applicants intend for the variousembodiments of the disclosure to be practiced otherwise thanspecifically described herein. Accordingly, this disclosure includes allmodifications and equivalents of the subject matter recited in theclaims appended hereto as permitted by applicable law. Moreover, anycombination of the above-described elements in all possible variationsthereof is encompassed by the disclosure unless otherwise indicatedherein or otherwise clearly contradicted by context.

Furthermore, numerous references have been made to patents and printedpublications throughout this specification. Each of the above-citedreferences and printed publications are individually incorporated hereinby reference in their entirety.

It is to be understood that the embodiments of the present disclosureare illustrative of the principles of the present disclosure. Othermodifications that may be employed are within the scope of thedisclosure. Thus, by way of example, but not of limitation, alternativeconfigurations of the present disclosure may be utilized in accordancewith the teachings herein. Accordingly, the present disclosure is notlimited to that precisely as shown and described.

The particulars shown herein are by way of example and for purposes ofillustrative discussion of the preferred embodiments of the presentdisclosure only and are presented in the cause of providing what isbelieved to be the most useful and readily understood description of theprinciples and conceptual aspects of various embodiments of thedisclosure.

It will be apparent to those having skill in the art that many changesmay be made to the details of the above-described embodiments withoutdeparting from the underlying principles of the disclosure. The scope ofthe present invention should, therefore, be determined only by thefollowing claims.

1. A method of cell-specifically labeling RNA molecules within aplurality of cells, the method comprising: (a) providing a plurality offixed, permeabilized cells in admixture in a well or compartment,wherein each of the plurality of cells comprises ribonucleic acid (RNA)molecules; (b) without lysing the cells, reverse transcribing the RNAmolecules within the plurality of cells, thereby generatingcomplementary deoxyribonucleic acid (cDNA) molecules within theplurality of cells, wherein primers used to reverse transcribe the RNAmolecules comprise a poly(T) sequence, a mix of random sequences, orboth a poly(T) sequence and a mix of random sequences, wherein eachprimer further comprises a first barcode sequence; wherein the firstbarcode sequence is specific to each well or compartment; (c) dividingthe plurality of cells comprising the cDNA molecules into a plurality ofprimary aliquots, wherein the plurality of primary aliquots comprises afirst primary aliquot and a second primary aliquot; (d) providingprimary nucleic acid tags comprising a second barcode sequence to theplurality of primary aliquots, wherein the primary nucleic acid tagscomprising a second barcode sequence provided to the first primaryaliquot are different in sequence from the primary nucleic acid tagsprovided to the second primary aliquot; (e) coupling the providedprimary nucleic acid tags comprising a second barcode sequence of (d) tothe cDNA molecules from each of the plurality of primary aliquots,thereby tagging the cDNA molecules with the primary nucleic acid tagscomprising a second barcode sequence and producing primary nucleicacid-tagged cDNA molecules, whereby the primary nucleic acid-tagged cDNAmolecules of the first primary aliquot are tagged with a differentprimary nucleic acid tag than the primary nucleic acid-tagged cDNAmolecules of the second primary aliquot.
 2. The method of claim 1,further comprising (f) combining the plurality of primary aliquots. 3.The method of claim 2, further comprising: (g) dividing the combinedprimary aliquots of (f) into a plurality of secondary aliquots, whereinthe plurality of secondary aliquots comprises a first secondary aliquotand a second secondary aliquot; (h) providing secondary nucleic acidtags comprising a third barcode sequence to the plurality of secondaryaliquots, wherein the secondary nucleic acid tags comprising a thirdbarcode sequence provided to the first secondary aliquot are differentin sequence from the secondary nucleic acid tags provided to the secondsecondary aliquot; and (i) coupling the provided secondary nucleic acidtags comprising a third barcode sequence of (h) to the primary nucleicacid-tagged cDNA molecules of (e) thereby tagging the primary nucleicacid-tagged cDNA molecules with the secondary nucleic acid tagscomprising a third barcode sequence and producing secondary nucleicacid-tagged cDNA molecules, whereby the secondary nucleic acid-taggedcDNA molecules of the first secondary aliquot are tagged with adifferent secondary nucleic acid tag than the secondary nucleicacid-tagged cDNA molecules of the second secondary aliquot.
 4. Themethod of claim 3, further comprising (j) repeating (f), (g), (h), and(i) with subsequent aliquots.
 5. The method of claim 4, wherein (j) isrepeated a number of times sufficient to generate a unique series ofnucleic acid tags for the cDNA molecules in a single cell of theplurality of cells.
 6. The method of claim 5, wherein the number oftimes is 1, 2, 3, 4, or
 5. 7. The method of claim 1, wherein each of theprimary nucleic acid tags comprises a first strand comprising the secondbarcode sequence.
 8. The method of claim 7, wherein each of the primarynucleic acid tags further comprises a 3′ hybridization sequence flankingthe 3′ end of the second barcode sequence, or a 5′ hybridizationsequence flanking the 5′ end of the second barcode sequence, or both. 9.The method of claim 3, wherein each of the secondary nucleic acid tagscomprises a first strand comprising the third barcode sequence.
 10. Themethod of claim 9, wherein each of the secondary nucleic acid tagsfurther comprises a 3′ hybridization sequence flanking the 3′ end of thethird barcode sequence, or a 5′ hybridization sequence flanking the 5′end of the third barcode sequence, or both.
 11. The method of claim 1,further comprising, prior to (a), hybridizing a single-stranded adaptersequence to each of the RNA molecules.
 12. The method of claim 1,further comprising, subsequent to (b), ligating an adapter sequence toeach of the cDNA molecules.
 13. The method of claim 1, furthercomprising, subsequent to (b), coupling an adapter sequence to each ofthe cDNA molecules by integrating the adapter sequence into the cDNAmolecules using a transposase and releasing the transposase to exposethe adapter sequence.
 14. The method of claim 3, further comprisingligating the primary nucleic acid tag of a primary nucleic acid-taggedcDNA molecule to the secondary nucleic acid tag.
 15. The method of claim12, wherein the ligation is performed within the plurality of cells. 16.The method of claim 3, further comprising removing primary nucleic acidtags or secondary nucleic acid tags that are unbound to the cDNAmolecules.
 17. The method of claim 4, wherein a final nucleic acid tagcoupled to the cDNA molecules comprises a capture agent.
 18. The methodof claim 3, further comprising lysing the plurality of cells to releasethe cDNA molecules from within the plurality of cells wherein the lysingis subsequent to (i).
 19. The method of claim 14, further comprisinglysing the plurality of cells to release the cDNA molecules from withinthe plurality of cells prior to the ligation.
 20. The method of claim19, wherein the lysing is subsequent to (i), and wherein a majority ofthe nucleic acid-tagged cDNA molecules from a single cell comprises thesame plurality of nucleic acid tags coupled thereto.
 21. The method ofclaim 1, wherein the plurality of cells is selected from the groupconsisting of mammalian cells, yeast cells, bacterial cells, andcombinations thereof.
 22. The method of claim 1, further comprising,prior to (a), ligating a single-stranded adapter sequence to each of theRNA molecules.
 23. The method of claim 22, wherein a 5′ end of thesingle-stranded adapter sequence is ligated to a 3′ end of an RNAmolecule or a 3′ end of the single-stranded adapter sequence is ligatedto a 5′ end of an RNA molecule.
 24. The method of claim 1, wherein theprimers comprise a poly(T) sequence.
 25. The method of claim 1, whereinthe primers comprise a random hexamer sequence.
 26. The method of claim12, further comprising providing the cDNA molecules with a plurality ofligation stop oligos complementary to the primary nucleic acid tagsafter ligating the primary nucleic acid tag.
 27. The method of claim 1,wherein the plurality of cells is fixed using formaldehyde.
 28. Themethod of claim 2, wherein combining the plurality of primary aliquotsincludes combining cells of the plurality of primary aliquots; andwherein dividing the combined primary aliquots of (f) into a pluralityof secondary aliquots includes dividing cells of the combined primaryaliquots in the plurality of secondary aliquots.
 29. The method of claim10, wherein each of the secondary nucleic acid tags further comprises asecond strand comprising: a first portion complementary to at least oneof the 5′ hybridization sequence, and a second portion complementary tothe 3′ hybridization sequence.